Merge pull request #260 from biowdl/deepvariant

Fix bugs in tasks for Deepvariant and WhatsHap

deepvariant.wdl

@@ -28,6 +28,7 @@ task RunDeepVariant {
         File inputBamIndex
         String modelType
         String outputVcf
+        String? postprocessVariantsExtraArgs
         File? customizedModel
         Int? numShards
         String? outputGVcf
@@ -51,8 +52,9 @@ task RunDeepVariant {
         ~{"--output_gvcf " + outputGVcf} \
         ~{"--customized_model " + customizedModel} \
         ~{"--num_shards " + numShards} \
-        ~{"--regions} " + regions} \
+        ~{"--regions "  + regions} \
         ~{"--sample_name " + sampleName} \
+        ~{"--postprocess_variants_extra_args " + postprocessVariantsExtraArgs} \
         ~{true="--vcf_stats_report" false="--novcf_stats_report" VCFStatsReport}
     }
 
@@ -83,6 +85,7 @@ task RunDeepVariant {
         regions: {description: "List of regions we want to process, in BED/BEDPE format.", category: "advanced"}
         sampleName: {description: "Sample name to use instead of the sample name from the input reads BAM (SM tag in the header).", category: "common"}
         VCFStatsReport: {description: "Output a visual report (HTML) of statistics about the output VCF.", category: "common"}
+        postprocessVariantsExtraArgs: {description: "A comma-separated list of flag_name=flag_value. 'flag_name' has to be valid flags for calpostprocess_variants.py.", category: "advanced"}
         memory: {description: "The amount of memory this job will use.", category: "advanced"}
         timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
         dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",

whatshap.wdl

@@ -45,6 +45,8 @@ task Phase {
     }
 
     command {
+        set -e
+
         whatshap phase \
         ~{vcf} \
         ~{phaseInput} \
@@ -56,7 +58,8 @@ task Phase {
         ~{if defined(sample) then ("--sample " +  '"' + sample + '"') else ""} \
         ~{if defined(chromosome) then ("--chromosome " +  '"' + chromosome + '"') else ""} \
         ~{if defined(threshold) then ("--threshold " +  '"' + threshold + '"') else ""} \
-        ~{if defined(ped) then ("--ped " +  '"' + ped + '"') else ""} \
+        ~{if defined(ped) then ("--ped " +  '"' + ped + '"') else ""}
+
         tabix -p vcf ~{outputVCF}
     }
 
@@ -159,13 +162,16 @@ task Haplotag {
     }
 
     command {
+        set -e
+
         whatshap haplotag \
           ~{vcf} \
           ~{alignments} \
           ~{if defined(outputFile) then ("--output " +  '"' + outputFile+ '"') else ""} \
           ~{if defined(reference) then ("--reference " +  '"' + reference + '"') else ""} \
           ~{if defined(regions) then ("--regions " +  '"' + regions + '"') else ""} \
-          ~{if defined(sample) then ("--sample " +  '"' + sample + '"') else ""} \
+          ~{if defined(sample) then ("--sample " +  '"' + sample + '"') else ""}
+
           python3 -c "import pysam; pysam.index('~{outputFile}')"
     }